BioC 3.5: CHECK report for DChIPRep on veracruz2

Package: DChIPRep

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DChIPRep_1.6.2.tar.gz

StartedAt: 2017-10-18 02:30:38 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:37:51 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 432.5 seconds

RetCode: 0

Status:  OK

CheckDir: DChIPRep.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DChIPRep_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DChIPRep.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DChIPRep/DESCRIPTION’ ... OK
* this is package ‘DChIPRep’ version ‘1.6.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DChIPRep’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotProfiles     8.065  0.062   8.368
plotSignificance 5.742  0.037   5.958
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DChIPRep.Rcheck/00check.log’
for details.

* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB

Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
* DONE (DChIPRep)

name	user	system	elapsed
DChIPRepResults	0.095	0.004	0.100
DESeq2Data	0.143	0.008	0.155
FDRresults	3.994	0.087	4.175
getMATfromDataFrame	1.459	0.029	1.516
importData	3.597	0.041	3.760
importDataFromMatrices	0.508	0.007	0.531
importData_soGGi	0.001	0.000	0.001
plotProfiles	8.065	0.062	8.368
plotSignificance	5.742	0.037	5.958
resultsDChIPRep	2.040	0.011	2.100
robust_mean	0.035	0.001	0.036
runTesting	2.638	0.015	2.708
show	2.071	0.011	2.147
summarizeCountsPerPosition	1.026	0.015	1.140